they probably measure the current going through the fan plug. If it is zero, and the 360 runs for longer than X amount of time (the amount of time it takes to overheat), then MS knows that you have been tinkering inside your 360, therefore violating XBL TOS, = ban.
Although it seems ridiculous to ban because of modding the fan, the only reasonable explanation I see is that they have failed in being able to detect backups (iXtreme 1.4 defeats all XBL checks, and most recent ban waves have accidentally banned unmodded boxes as well), so their only way to detect modified consoles is the fact that if you have done the 12v mod you have opened your 360, and are therefore much more likely to flash your drive.
I'm sure the 360 relays all kinds of information back to MS so they can get statistical data on the 360's performance
CPU, GPU temps, console orientation (horizontal, vertical), fan voltage, fan current, devices connected, etc.